Last updated: 2021-02-18

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Knit directory: melanoma_publication_old_data/

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Preparations

Here, we add more metadata and colData annotations to the SCE object which are needed for downstream analyses.

Load libraries

library(SingleCellExperiment)
library(dplyr)

Load data

sce <- readRDS(file = "data/data_for_analysis/sce_protein.rds")
cur_sce <- data.frame(colData(sce))
cur_meta <- data.frame(metadata(sce))

Add existing clinical colData

Various variables

cur_sce <- cur_sce %>%
  left_join(., cur_meta[,c("ImageNumber", "Location", "Adjuvant", "IHC_T_score", "Mutation", 
                           "Cancer_Stage", "Status_at_3m", "BlockID", "Description", "TissueType",
                           "MM_location", "Age_range", "Gender", "PatientID", "relapse")])
Joining, by = "ImageNumber"
colData(sce)$Location <- cur_sce$Location
colData(sce)$Adjuvant <- cur_sce$Adjuvant
colData(sce)$E_I_D <- cur_sce$IHC_T_score
colData(sce)$Mutation <- cur_sce$Mutation
colData(sce)$Cancer_Stage <- cur_sce$Cancer_Stage
colData(sce)$Status_at_3m <- cur_sce$Status_at_3m
colData(sce)$BlockID <- cur_sce$BlockID
colData(sce)$Description <- cur_sce$Description
colData(sce)$TissueType <- cur_sce$TissueType
colData(sce)$MM_location <- cur_sce$MM_location
colData(sce)$Age <- cur_sce$Age_range
colData(sce)$Gender <- cur_sce$Gender
colData(sce)$PatientID <- cur_sce$PatientID
colData(sce)$relapse <- cur_sce$relapse

Make clinical data interpretable for statistical analysis

Simplified biopsy origin

# create simplified location of biopsies
cur_sce$MM_location_simplified <- NA
cur_sce[grep("CTRL", cur_sce$Location), ]$MM_location_simplified <- "control"
cur_sce[grep("LN", cur_sce$MM_location), ]$MM_location_simplified <- "LN"
cur_sce[grep("skin", cur_sce$MM_location), ]$MM_location_simplified <- "skin"
cur_sce[is.na(cur_sce$MM_location_simplified) == TRUE, ]$MM_location_simplified <- "other"

# add to colData
colData(sce)$MM_location_simplified <- cur_sce$MM_location_simplified

# add to metadata
cur_meta <- left_join(cur_meta, distinct(cur_sce, MM_location_simplified, ImageNumber))
Joining, by = "ImageNumber"

Create therapy grouping before surgery

# unique treatments
unique(cur_meta$Last_sys_treatment_before_surgery)
 [1] "BRAFi + MEKi"          "aPD1"                  "untreated"            
 [4] "aPD1 + aCTLA4 or aPD1" "aPD1 + aCTLA4"         "chemotherapy"         
 [7] "aPD1 + aLAG3"          NA                      "aCTLA4"               
[10] "MEKi"                 
# group treatment types
cur_meta$treatment_group_before_surgery <- NA
cur_meta[cur_meta$MM_location_simplified == "control",]$treatment_group_before_surgery <- "control"
cur_meta[cur_meta$Last_sys_treatment_before_surgery %in% "untreated",]$treatment_group_before_surgery <- "untreated"
cur_meta[cur_meta$Last_sys_treatment_before_surgery %in% c("aPD1", "aPD1 + aCTLA4", "aCTLA4", 
                                                           "aPD1 + aCTLA4 or aPD1", "aPD1 + aLAG3"),]$treatment_group_before_surgery <- "ICI"
cur_meta[cur_meta$Last_sys_treatment_before_surgery %in% c("BRAFi + MEKi", "MEKi"),]$treatment_group_before_surgery <- "Targeted"
cur_meta[cur_meta$Last_sys_treatment_before_surgery %in% c("chemotherapy"),]$treatment_group_before_surgery <- "Chemotherapy"
cur_meta[is.na(cur_meta$Last_sys_treatment_before_surgery),]$treatment_group_before_surgery <- "unknown"

# add treatment type  to cur_sce
cur_sce <- left_join(cur_sce, cur_meta[,c("ImageNumber", "treatment_group_before_surgery")])
Joining, by = "ImageNumber"
# add relapse to SCE
colData(sce)$treatment_group_before_surgery <- cur_sce$treatment_group_before_surgery

Create therapy grouping after surgery

# unique treatments
unique(cur_meta$Treatment_after_surgery)
 [1] "BRAFi + MEKi"          "aCTLA4"                "BRAFi + MEKi +/- aPD1"
 [4] "aPD1 + aCTLA4"         "aPD1"                  "untreated"            
 [7] "chemotherapy"          NA                      "MEKi"                 
[10] "BRAFi"                 "TVEC"                  "aPD1 + aLAG3"         
[13] "PC"                   
# group treatment types
cur_meta$treatment_group_after_surgery <- NA
cur_meta[cur_meta$MM_location_simplified == "control",]$treatment_group_after_surgery <- "control"
cur_meta[cur_meta$Treatment_after_surgery %in% "untreated",]$treatment_group_after_surgery <- "untreated"
cur_meta[cur_meta$Treatment_after_surgery %in% c("aPD1 + aCTLA4", "aPD1", "aCTLA4", "aPD1 + aLAG3"),]$treatment_group_after_surgery <- "ICI"
cur_meta[cur_meta$Treatment_after_surgery %in% c("BRAFi + MEKi", "BRAFi", "MEKi", "BRAFi + MEKi +/- aPD1"),]$treatment_group_after_surgery <- "Targeted"
cur_meta[cur_meta$Treatment_after_surgery %in% c("chemotherapy"),]$treatment_group_after_surgery <- "Chemotherapy"
cur_meta[cur_meta$Treatment_after_surgery %in% c("TVEC"),]$treatment_group_after_surgery <- "TVEC"
cur_meta[cur_meta$Treatment_after_surgery %in% c("PC"),]$treatment_group_after_surgery <- "Palliative"
cur_meta[is.na(cur_meta$Treatment_after_surgery),]$treatment_group_after_surgery <- "unknown"

# add treatment type  to cur_sce
cur_sce <- left_join(cur_sce, cur_meta[,c("ImageNumber", "treatment_group_after_surgery")])
Joining, by = "ImageNumber"
# add relapse to SCE
colData(sce)$treatment_group_after_surgery <- cur_sce$treatment_group_after_surgery

Create binarized grouping based on number of treatments before surgery

cur_meta$treatment_status_before_surgery <- NA
cur_meta[cur_meta$Location == "CTRL",]$treatment_status_before_surgery <- "control"
cur_meta[cur_meta$Location != "CTRL",]$treatment_status_before_surgery <- ifelse(cur_meta[cur_meta$Location != "CTRL",]$Nr_treatments_before_surgery == 0, "naive", "non-naive")

# add treatment type to cur_sce
cur_sce <- left_join(cur_sce, cur_meta[,c("ImageNumber", "treatment_status_before_surgery")])
Joining, by = "ImageNumber"
# add to SCE
colData(sce)$treatment_status_before_surgery <- cur_sce$treatment_status_before_surgery

Create Death grouping

Date_death <- metadata(sce)$Date_death
sce$Date_death <- Date_death[sce$ImageNumber]

#binarize death
sce$Death <- "no"
sce[,grepl("20",sce$Date_death)]$Death <- "yes"

Add updated metadata to SCE object

metadata(sce) <- as.list(cur_meta)

Save the SCE object

saveRDS(sce,file = "data/data_for_analysis/sce_protein.rds")

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] dplyr_1.0.2                 SingleCellExperiment_1.12.0
 [3] SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [5] GenomicRanges_1.42.0        GenomeInfoDb_1.26.2        
 [7] IRanges_2.24.1              S4Vectors_0.28.1           
 [9] BiocGenerics_0.36.0         MatrixGenerics_1.2.0       
[11] matrixStats_0.57.0          workflowr_1.6.2            

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5             XVector_0.30.0         pillar_1.4.7          
 [4] compiler_4.0.3         later_1.1.0.1          git2r_0.28.0          
 [7] zlibbioc_1.36.0        bitops_1.0-6           tools_4.0.3           
[10] digest_0.6.27          lattice_0.20-41        evaluate_0.14         
[13] lifecycle_0.2.0        tibble_3.0.4           pkgconfig_2.0.3       
[16] rlang_0.4.10           Matrix_1.3-2           DelayedArray_0.16.0   
[19] rstudioapi_0.13        yaml_2.2.1             xfun_0.20             
[22] GenomeInfoDbData_1.2.4 stringr_1.4.0          knitr_1.30            
[25] generics_0.1.0         fs_1.5.0               vctrs_0.3.6           
[28] tidyselect_1.1.0       grid_4.0.3             rprojroot_2.0.2       
[31] glue_1.4.2             R6_2.5.0               rmarkdown_2.6         
[34] purrr_0.3.4            magrittr_2.0.1         whisker_0.4           
[37] promises_1.1.1         ellipsis_0.3.1         htmltools_0.5.0       
[40] httpuv_1.5.4           stringi_1.5.3          RCurl_1.98-1.2        
[43] crayon_1.3.4